RNA Structural Forms Studied by Vibrational Circular Dichroism:  Ab Initio Interpretation of the Spectra

Abstract

Infrared (IR) and vibrational circular dichroism (VCD) spectra of single-stranded poly(rA) and poly(rU) RNA polynucleotides and double-and triple-stranded RNA helices were recorded and interpreted on the basis of density functional theory (DFT) at the BPW91/6-31G** level. Ab initio computations were performed for smaller fragments and extended to longer oligomers via transfer of atomic property tensors. The normal mode partial optimization method developed lately was found convenient for relaxation of the fragment geometries. Most of observed spectral features could be assigned to vibrations of the adenine, uracil, and sugar-phosphate chromophores; in particular, the VCD band shapes could be explained on the basis of specific spatial interactions. Thus, the VCD technique proved to be sensitive to various RNA conformational types (random coil, single strand, duplex, and triplex) in solution, spectra of which could be reliably modeled. The effect of the solvent could be only partially included, and ambiguity remains in the model structure used for the triplex RNA form.

Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study

“…[28][29][30][31] In the past, such computations provided preferential geometries and binding sites and could explain different DNA affinity to different metals. [32][33][34] Because of the computational limits, the modeling is often restricted to simplified nucleic acid components.…”

“…Although it may not be essential for evaluation of relative energies associated with some nonelectrostatic metal-nucleobase interactions, 32 a proper solvent model is crucial for the estimation of the vibrational frequencies, particularly for vibrations of the polar groups of the nucleic acids. 28 Typically, polarized continuum models (PCM) are used in such studies, which can be implemented very efficiently in available computational codes. 41,42 Ultimately, we test the preferred and specific binding sites of the dGMP molecule ( Figure 1) for different metal ions.…”

Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides

“…Similar problems with the modeling of this vibrational motion were found in other studies, since the vibration is anharmonic, susceptible to formation of strong hydrogen bonds with the solvent or other molecular parts, and the polar CdO group strongly polarizes its environment. 29,36,67 Apparently, the CdO stretching signal (centered in a vacuum around 1716 cm -1 ) moved to lower wavenumbers for the explicit model, but still is deviating by ∼40 cm -1 from experiment. Positions of the base ring deformation modes (∼1500-1660 cm -1 ) are less influenced by the solvent, nevertheless the intensity profile changes under hydration.…”

“…Principle features of experimental RNA and DNA spectra have been described in numerous studies previously 3,4,14,15,17,18,23,26,28,29,40 and we recapitulate them only briefly. The CdO stretching region of the bases (1600-1700 cm -1 ) gives rise to a strong absorption, while relatively minor distinct features can be found in the mid-IR region of 1150-1500 cm -1 , additionally perturbed by D 2 O absorption (around 1220 cm -1 ).…”

“…28, 29 It should be also noted that the normal-mode restricted optimization method 31 used in this study is indispensable for the simulations and improved the sugar-phosphate signal against the conventional torsion-angle restriction used previously. 28,29 The normal mode method provided more stable optimization trajectories, faster convergence and better spectral profiles namely for the clusters containing hydrogen bonds. Unfortunately, the other simplified models, the regular geometry with (trace b in Figure 6) and without (trace c) solvent, are much less satisfying.…”